You signed in with another tab or window. Reload to refresh your session.You signed out in another tab or window. Reload to refresh your session.You switched accounts on another tab or window. Reload to refresh your session.Dismiss alert
I am learning to train OpenFold-Multimer using just the alignments and mmcifs provided by AlphaFold/OpenFold. I used the following command to run the training, which I found to run fine when I train the monomer version of OpenFold:
Traceback (most recent call last):
File "/lustre/scratch5/.mdt0/hungd238/Fold-21-Multimer/fold-21/train_openfold.py", line 703, in
main(args)
File "/lustre/scratch5/.mdt0/hungd238/Fold-21-Multimer/fold-21/train_openfold.py", line 356, in main
data_module.setup()
File "/lustre/scratch5/.mdt0/hungd238/Fold-21-Multimer/fold-21/openfold/data/data_modules.py", line 1139, in setup
self.train_dataset = OpenFoldMultimerDataset(
File "/lustre/scratch5/.mdt0/hungd238/Fold-21-Multimer/fold-21/openfold/data/data_modules.py", line 678, in init
super(OpenFoldMultimerDataset, self).init(datasets=datasets,
File "/lustre/scratch5/.mdt0/hungd238/Fold-21-Multimer/fold-21/openfold/data/data_modules.py", line 557, in init
self.reroll()
File "/lustre/scratch5/.mdt0/hungd238/Fold-21-Multimer/fold-21/openfold/data/data_modules.py", line 660, in reroll
datapoint_idx = next(samples)
File "/lustre/scratch5/.mdt0/hungd238/Fold-21-Multimer/fold-21/openfold/data/data_modules.py", line 725, in looped_samples
mmcif_data_cache = dataset.mmcif_data_cache
AttributeError: 'OpenFoldSingleMultimerDataset' object has no attribute 'mmcif_data_cache'. Did you mean: 'mmcif_data_cache_path'?
Traceback (most recent call last):
File "/lustre/scratch5/.mdt0/hungd238/Fold-21-Multimer/fold-21/train_openfold.py", line 703, in
main(args)
File "/lustre/scratch5/.mdt0/hungd238/Fold-21-Multimer/fold-21/train_openfold.py", line 356, in main
data_module.setup()
File "/lustre/scratch5/.mdt0/hungd238/Fold-21-Multimer/fold-21/openfold/data/data_modules.py", line 1139, in setup
self.train_dataset = OpenFoldMultimerDataset(
File "/lustre/scratch5/.mdt0/hungd238/Fold-21-Multimer/fold-21/openfold/data/data_modules.py", line 678, in init
super(OpenFoldMultimerDataset, self).init(datasets=datasets,
File "/lustre/scratch5/.mdt0/hungd238/Fold-21-Multimer/fold-21/openfold/data/data_modules.py", line 557, in init
self.reroll()
File "/lustre/scratch5/.mdt0/hungd238/Fold-21-Multimer/fold-21/openfold/data/data_modules.py", line 660, in reroll
datapoint_idx = next(samples)
File "/lustre/scratch5/.mdt0/hungd238/Fold-21-Multimer/fold-21/openfold/data/data_modules.py", line 725, in looped_samples
mmcif_data_cache = dataset.mmcif_data_cache
AttributeError: 'OpenFoldSingleMultimerDataset' object has no attribute 'mmcif_data_cache'. Did you mean: 'mmcif_data_cache_path'?
srun: error: nid001388: task 5: Exited with exit code 1
srun: Terminating StepId=21060918.0
I changed dataset.mmcif_data_cache to dataset.mmcif_data_cache_path in the file openfold/data/data_modules.py but then I ran into another error:
Traceback (most recent call last):
File "/lustre/scratch5/.mdt0/hungd238/Fold-21-Multimer/fold-21/train_openfold.py", line 703, in
main(args)
File "/lustre/scratch5/.mdt0/hungd238/Fold-21-Multimer/fold-21/train_openfold.py", line 356, in main
data_module.setup()
File "/lustre/scratch5/.mdt0/hungd238/Fold-21-Multimer/fold-21/openfold/data/data_modules.py", line 1139, in setup
self.train_dataset = OpenFoldMultimerDataset(
File "/lustre/scratch5/.mdt0/hungd238/Fold-21-Multimer/fold-21/openfold/data/data_modules.py", line 678, in init
Traceback (most recent call last):
File "/lustre/scratch5/.mdt0/hungd238/Fold-21-Multimer/fold-21/train_openfold.py", line 703, in
super(OpenFoldMultimerDataset, self).init(datasets=datasets,
File "/lustre/scratch5/.mdt0/hungd238/Fold-21-Multimer/fold-21/openfold/data/data_modules.py", line 557, in init
self.reroll()
File "/lustre/scratch5/.mdt0/hungd238/Fold-21-Multimer/fold-21/openfold/data/data_modules.py", line 660, in reroll
main(args)
File "/lustre/scratch5/.mdt0/hungd238/Fold-21-Multimer/fold-21/train_openfold.py", line 356, in main
datapoint_idx = next(samples)
File "/lustre/scratch5/.mdt0/hungd238/Fold-21-Multimer/fold-21/openfold/data/data_modules.py", line 732, in looped_samples
data_module.setup()
File "/lustre/scratch5/.mdt0/hungd238/Fold-21-Multimer/fold-21/openfold/data/data_modules.py", line 1139, in setup
mmcif_data_cache_entry = mmcif_data_cache[mmcif_id]
TypeError: 'NoneType' object is not subscriptable
self.train_dataset = OpenFoldMultimerDataset(
File "/lustre/scratch5/.mdt0/hungd238/Fold-21-Multimer/fold-21/openfold/data/data_modules.py", line 678, in init
super(OpenFoldMultimerDataset, self).init(datasets=datasets,
File "/lustre/scratch5/.mdt0/hungd238/Fold-21-Multimer/fold-21/openfold/data/data_modules.py", line 557, in init
self.reroll()
File "/lustre/scratch5/.mdt0/hungd238/Fold-21-Multimer/fold-21/openfold/data/data_modules.py", line 660, in reroll
datapoint_idx = next(samples)
File "/lustre/scratch5/.mdt0/hungd238/Fold-21-Multimer/fold-21/openfold/data/data_modules.py", line 732, in looped_samples
mmcif_data_cache_entry = mmcif_data_cache[mmcif_id]
TypeError: 'NoneType' object is not subscriptable
Traceback (most recent call last):
File "/lustre/scratch5/.mdt0/hungd238/Fold-21-Multimer/fold-21/train_openfold.py", line 703, in
main(args)
File "/lustre/scratch5/.mdt0/hungd238/Fold-21-Multimer/fold-21/train_openfold.py", line 356, in main
data_module.setup()
File "/lustre/scratch5/.mdt0/hungd238/Fold-21-Multimer/fold-21/openfold/data/data_modules.py", line 1139, in setup
self.train_dataset = OpenFoldMultimerDataset(
File "/lustre/scratch5/.mdt0/hungd238/Fold-21-Multimer/fold-21/openfold/data/data_modules.py", line 678, in init
super(OpenFoldMultimerDataset, self).init(datasets=datasets,
File "/lustre/scratch5/.mdt0/hungd238/Fold-21-Multimer/fold-21/openfold/data/data_modules.py", line 557, in init
self.reroll()
File "/lustre/scratch5/.mdt0/hungd238/Fold-21-Multimer/fold-21/openfold/data/data_modules.py", line 660, in reroll
datapoint_idx = next(samples)
File "/lustre/scratch5/.mdt0/hungd238/Fold-21-Multimer/fold-21/openfold/data/data_modules.py", line 732, in looped_samples
mmcif_data_cache_entry = mmcif_data_cache[mmcif_id]
TypeError: 'NoneType' object is not subscriptable
Traceback (most recent call last):
File "/lustre/scratch5/.mdt0/hungd238/Fold-21-Multimer/fold-21/train_openfold.py", line 703, in
main(args)
File "/lustre/scratch5/.mdt0/hungd238/Fold-21-Multimer/fold-21/train_openfold.py", line 356, in main
data_module.setup()
File "/lustre/scratch5/.mdt0/hungd238/Fold-21-Multimer/fold-21/openfold/data/data_modules.py", line 1139, in setup
self.train_dataset = OpenFoldMultimerDataset(
File "/lustre/scratch5/.mdt0/hungd238/Fold-21-Multimer/fold-21/openfold/data/data_modules.py", line 678, in init
super(OpenFoldMultimerDataset, self).init(datasets=datasets,
File "/lustre/scratch5/.mdt0/hungd238/Fold-21-Multimer/fold-21/openfold/data/data_modules.py", line 557, in init
self.reroll()
File "/lustre/scratch5/.mdt0/hungd238/Fold-21-Multimer/fold-21/openfold/data/data_modules.py", line 660, in reroll
datapoint_idx = next(samples)
File "/lustre/scratch5/.mdt0/hungd238/Fold-21-Multimer/fold-21/openfold/data/data_modules.py", line 732, in looped_samples
mmcif_data_cache_entry = mmcif_data_cache[mmcif_id]
TypeError: 'NoneType' object is not subscriptable
Traceback (most recent call last):
File "/lustre/scratch5/.mdt0/hungd238/Fold-21-Multimer/fold-21/train_openfold.py", line 703, in
main(args)
File "/lustre/scratch5/.mdt0/hungd238/Fold-21-Multimer/fold-21/train_openfold.py", line 356, in main
data_module.setup()
File "/lustre/scratch5/.mdt0/hungd238/Fold-21-Multimer/fold-21/openfold/data/data_modules.py", line 1139, in setup
self.train_dataset = OpenFoldMultimerDataset(
File "/lustre/scratch5/.mdt0/hungd238/Fold-21-Multimer/fold-21/openfold/data/data_modules.py", line 678, in init
super(OpenFoldMultimerDataset, self).init(datasets=datasets,
File "/lustre/scratch5/.mdt0/hungd238/Fold-21-Multimer/fold-21/openfold/data/data_modules.py", line 557, in init
self.reroll()
File "/lustre/scratch5/.mdt0/hungd238/Fold-21-Multimer/fold-21/openfold/data/data_modules.py", line 660, in reroll
datapoint_idx = next(samples)
File "/lustre/scratch5/.mdt0/hungd238/Fold-21-Multimer/fold-21/openfold/data/data_modules.py", line 732, in looped_samples
mmcif_data_cache_entry = mmcif_data_cache[mmcif_id]
TypeError: 'NoneType' object is not subscriptable
srun: error: nid001385: tasks 2-3: Exited with exit code 1
srun: Terminating StepId=21060799.0
Do you have any suggestions on how to fix these issues? Thank you in advance.
The text was updated successfully, but these errors were encountered:
Hi,
I am learning to train OpenFold-Multimer using just the alignments and mmcifs provided by AlphaFold/OpenFold. I used the following command to run the training, which I found to run fine when I train the monomer version of OpenFold:
python train_openfold.py pdb_data/mmcif_files alignment_data/alignments/ pdb_data/mmcif_files/ multimer/ 2021-10-10 --train_chain_data_cache_path pdb_data/data_caches/chain_data_cache.json --template_release_dates_cache_path pdb_data/data_caches/mmcif_cache.json --config_preset "model_1_multimer_v3" --obsolete_pdbs_file_path pdb_data/obsolete.dat --num_nodes 4 --seed 121924 --gpus 16 --max_epochs 15 --precision bf16-mixed
However, I keep running into the following error:
Traceback (most recent call last):
File "/lustre/scratch5/.mdt0/hungd238/Fold-21-Multimer/fold-21/train_openfold.py", line 703, in
main(args)
File "/lustre/scratch5/.mdt0/hungd238/Fold-21-Multimer/fold-21/train_openfold.py", line 356, in main
data_module.setup()
File "/lustre/scratch5/.mdt0/hungd238/Fold-21-Multimer/fold-21/openfold/data/data_modules.py", line 1139, in setup
self.train_dataset = OpenFoldMultimerDataset(
File "/lustre/scratch5/.mdt0/hungd238/Fold-21-Multimer/fold-21/openfold/data/data_modules.py", line 678, in init
super(OpenFoldMultimerDataset, self).init(datasets=datasets,
File "/lustre/scratch5/.mdt0/hungd238/Fold-21-Multimer/fold-21/openfold/data/data_modules.py", line 557, in init
self.reroll()
File "/lustre/scratch5/.mdt0/hungd238/Fold-21-Multimer/fold-21/openfold/data/data_modules.py", line 660, in reroll
datapoint_idx = next(samples)
File "/lustre/scratch5/.mdt0/hungd238/Fold-21-Multimer/fold-21/openfold/data/data_modules.py", line 725, in looped_samples
mmcif_data_cache = dataset.mmcif_data_cache
AttributeError: 'OpenFoldSingleMultimerDataset' object has no attribute 'mmcif_data_cache'. Did you mean: 'mmcif_data_cache_path'?
Traceback (most recent call last):
File "/lustre/scratch5/.mdt0/hungd238/Fold-21-Multimer/fold-21/train_openfold.py", line 703, in
main(args)
File "/lustre/scratch5/.mdt0/hungd238/Fold-21-Multimer/fold-21/train_openfold.py", line 356, in main
data_module.setup()
File "/lustre/scratch5/.mdt0/hungd238/Fold-21-Multimer/fold-21/openfold/data/data_modules.py", line 1139, in setup
self.train_dataset = OpenFoldMultimerDataset(
File "/lustre/scratch5/.mdt0/hungd238/Fold-21-Multimer/fold-21/openfold/data/data_modules.py", line 678, in init
super(OpenFoldMultimerDataset, self).init(datasets=datasets,
File "/lustre/scratch5/.mdt0/hungd238/Fold-21-Multimer/fold-21/openfold/data/data_modules.py", line 557, in init
self.reroll()
File "/lustre/scratch5/.mdt0/hungd238/Fold-21-Multimer/fold-21/openfold/data/data_modules.py", line 660, in reroll
datapoint_idx = next(samples)
File "/lustre/scratch5/.mdt0/hungd238/Fold-21-Multimer/fold-21/openfold/data/data_modules.py", line 725, in looped_samples
mmcif_data_cache = dataset.mmcif_data_cache
AttributeError: 'OpenFoldSingleMultimerDataset' object has no attribute 'mmcif_data_cache'. Did you mean: 'mmcif_data_cache_path'?
srun: error: nid001388: task 5: Exited with exit code 1
srun: Terminating StepId=21060918.0
I changed
dataset.mmcif_data_cache
todataset.mmcif_data_cache_path
in the fileopenfold/data/data_modules.py
but then I ran into another error:Traceback (most recent call last):
File "/lustre/scratch5/.mdt0/hungd238/Fold-21-Multimer/fold-21/train_openfold.py", line 703, in
main(args)
File "/lustre/scratch5/.mdt0/hungd238/Fold-21-Multimer/fold-21/train_openfold.py", line 356, in main
data_module.setup()
File "/lustre/scratch5/.mdt0/hungd238/Fold-21-Multimer/fold-21/openfold/data/data_modules.py", line 1139, in setup
self.train_dataset = OpenFoldMultimerDataset(
File "/lustre/scratch5/.mdt0/hungd238/Fold-21-Multimer/fold-21/openfold/data/data_modules.py", line 678, in init
Traceback (most recent call last):
File "/lustre/scratch5/.mdt0/hungd238/Fold-21-Multimer/fold-21/train_openfold.py", line 703, in
super(OpenFoldMultimerDataset, self).init(datasets=datasets,
File "/lustre/scratch5/.mdt0/hungd238/Fold-21-Multimer/fold-21/openfold/data/data_modules.py", line 557, in init
self.reroll()
File "/lustre/scratch5/.mdt0/hungd238/Fold-21-Multimer/fold-21/openfold/data/data_modules.py", line 660, in reroll
main(args)
File "/lustre/scratch5/.mdt0/hungd238/Fold-21-Multimer/fold-21/train_openfold.py", line 356, in main
datapoint_idx = next(samples)
File "/lustre/scratch5/.mdt0/hungd238/Fold-21-Multimer/fold-21/openfold/data/data_modules.py", line 732, in looped_samples
data_module.setup()
File "/lustre/scratch5/.mdt0/hungd238/Fold-21-Multimer/fold-21/openfold/data/data_modules.py", line 1139, in setup
mmcif_data_cache_entry = mmcif_data_cache[mmcif_id]
TypeError: 'NoneType' object is not subscriptable
self.train_dataset = OpenFoldMultimerDataset(
File "/lustre/scratch5/.mdt0/hungd238/Fold-21-Multimer/fold-21/openfold/data/data_modules.py", line 678, in init
super(OpenFoldMultimerDataset, self).init(datasets=datasets,
File "/lustre/scratch5/.mdt0/hungd238/Fold-21-Multimer/fold-21/openfold/data/data_modules.py", line 557, in init
self.reroll()
File "/lustre/scratch5/.mdt0/hungd238/Fold-21-Multimer/fold-21/openfold/data/data_modules.py", line 660, in reroll
datapoint_idx = next(samples)
File "/lustre/scratch5/.mdt0/hungd238/Fold-21-Multimer/fold-21/openfold/data/data_modules.py", line 732, in looped_samples
mmcif_data_cache_entry = mmcif_data_cache[mmcif_id]
TypeError: 'NoneType' object is not subscriptable
Traceback (most recent call last):
File "/lustre/scratch5/.mdt0/hungd238/Fold-21-Multimer/fold-21/train_openfold.py", line 703, in
main(args)
File "/lustre/scratch5/.mdt0/hungd238/Fold-21-Multimer/fold-21/train_openfold.py", line 356, in main
data_module.setup()
File "/lustre/scratch5/.mdt0/hungd238/Fold-21-Multimer/fold-21/openfold/data/data_modules.py", line 1139, in setup
self.train_dataset = OpenFoldMultimerDataset(
File "/lustre/scratch5/.mdt0/hungd238/Fold-21-Multimer/fold-21/openfold/data/data_modules.py", line 678, in init
super(OpenFoldMultimerDataset, self).init(datasets=datasets,
File "/lustre/scratch5/.mdt0/hungd238/Fold-21-Multimer/fold-21/openfold/data/data_modules.py", line 557, in init
self.reroll()
File "/lustre/scratch5/.mdt0/hungd238/Fold-21-Multimer/fold-21/openfold/data/data_modules.py", line 660, in reroll
datapoint_idx = next(samples)
File "/lustre/scratch5/.mdt0/hungd238/Fold-21-Multimer/fold-21/openfold/data/data_modules.py", line 732, in looped_samples
mmcif_data_cache_entry = mmcif_data_cache[mmcif_id]
TypeError: 'NoneType' object is not subscriptable
Traceback (most recent call last):
File "/lustre/scratch5/.mdt0/hungd238/Fold-21-Multimer/fold-21/train_openfold.py", line 703, in
main(args)
File "/lustre/scratch5/.mdt0/hungd238/Fold-21-Multimer/fold-21/train_openfold.py", line 356, in main
data_module.setup()
File "/lustre/scratch5/.mdt0/hungd238/Fold-21-Multimer/fold-21/openfold/data/data_modules.py", line 1139, in setup
self.train_dataset = OpenFoldMultimerDataset(
File "/lustre/scratch5/.mdt0/hungd238/Fold-21-Multimer/fold-21/openfold/data/data_modules.py", line 678, in init
super(OpenFoldMultimerDataset, self).init(datasets=datasets,
File "/lustre/scratch5/.mdt0/hungd238/Fold-21-Multimer/fold-21/openfold/data/data_modules.py", line 557, in init
self.reroll()
File "/lustre/scratch5/.mdt0/hungd238/Fold-21-Multimer/fold-21/openfold/data/data_modules.py", line 660, in reroll
datapoint_idx = next(samples)
File "/lustre/scratch5/.mdt0/hungd238/Fold-21-Multimer/fold-21/openfold/data/data_modules.py", line 732, in looped_samples
mmcif_data_cache_entry = mmcif_data_cache[mmcif_id]
TypeError: 'NoneType' object is not subscriptable
Traceback (most recent call last):
File "/lustre/scratch5/.mdt0/hungd238/Fold-21-Multimer/fold-21/train_openfold.py", line 703, in
main(args)
File "/lustre/scratch5/.mdt0/hungd238/Fold-21-Multimer/fold-21/train_openfold.py", line 356, in main
data_module.setup()
File "/lustre/scratch5/.mdt0/hungd238/Fold-21-Multimer/fold-21/openfold/data/data_modules.py", line 1139, in setup
self.train_dataset = OpenFoldMultimerDataset(
File "/lustre/scratch5/.mdt0/hungd238/Fold-21-Multimer/fold-21/openfold/data/data_modules.py", line 678, in init
super(OpenFoldMultimerDataset, self).init(datasets=datasets,
File "/lustre/scratch5/.mdt0/hungd238/Fold-21-Multimer/fold-21/openfold/data/data_modules.py", line 557, in init
self.reroll()
File "/lustre/scratch5/.mdt0/hungd238/Fold-21-Multimer/fold-21/openfold/data/data_modules.py", line 660, in reroll
datapoint_idx = next(samples)
File "/lustre/scratch5/.mdt0/hungd238/Fold-21-Multimer/fold-21/openfold/data/data_modules.py", line 732, in looped_samples
mmcif_data_cache_entry = mmcif_data_cache[mmcif_id]
TypeError: 'NoneType' object is not subscriptable
srun: error: nid001385: tasks 2-3: Exited with exit code 1
srun: Terminating StepId=21060799.0
Do you have any suggestions on how to fix these issues? Thank you in advance.
The text was updated successfully, but these errors were encountered: